rs10733517

Variant names:

• chr9-5883409-G-C
• rs10733517
• ENST00000436015.6:n.*231-1734C>G

Your query was ambiguous. Multiple possible variants found:

• chr9-5883409-G-C
• chr9-5883409-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000436015.6(BRD10):​n.*231-1734C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 26)
• Consequence: BRD10 ENST00000436015.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314
• Publications: 1 publications found

Genes affected

BRD10 (HGNC:23378): (bromodomain containing 10)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRD10	XR_007061249.1	n.6353-1734C>G		intron_variant	Intron 9 of 10
BRD10	XR_007061250.1	n.6353-1734C>G		intron_variant	Intron 9 of 9
BRD10	XR_007061251.1	n.6241-1734C>G		intron_variant	Intron 9 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRD10	ENST00000436015.6	n.*231-1734C>G		intron_variant	Intron 3 of 3	3		ENSP00000438370.1

Frequencies

GnomAD3 genomes Cov.: 26

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 26

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.20
DANN	Benign	0.61
PhyloP100		-0.31

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10733517; hg19: chr9-5883409;